SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips

[1]  A. Oshlack,et al.  SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips , 2012, Genome Biology.

[2]  J. Maksimovic,et al.  Genome-scale profiling reveals a subset of genes regulated by DNA methylation that program somatic T-cell phenotypes in humans , 2012, Genes and Immunity.

[3]  C. Sotiriou,et al.  Evaluation of the Infinium Methylation 450K technology. , 2011, Epigenomics.

[4]  K. Gunderson,et al.  High density DNA methylation array with single CpG site resolution. , 2011, Genomics.

[5]  Xiao Zhang,et al.  Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis , 2010, BMC Bioinformatics.

[6]  Zhijin Wu,et al.  Subset Quantile Normalization Using Negative Control Features , 2010, J. Comput. Biol..

[7]  Stephan Beck,et al.  Taking the measure of the methylome , 2010, Nature Biotechnology.

[8]  T. Huang,et al.  Profiling DNA Methylomes from Microarray to Genome-Scale Sequencing , 2010, Technology in cancer research & treatment.

[9]  Jian-Bing Fan,et al.  Genome‐wide DNA methylation profiling , 2010, Wiley interdisciplinary reviews. Systems biology and medicine.

[10]  G. Tsujimoto,et al.  Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing , 2010, BMC Genomics.

[11]  P. Laird.  Principles and challenges of genome-wide DNA methylation analysis , 2010, Nature Reviews Genetics.

[12]  Lee E. Edsall,et al.  Human DNA methylomes at base resolution show widespread epigenomic differences , 2009, Nature.

[13]  K. Gunderson,et al.  Genome-wide DNA methylation profiling using Infinium® assay. , 2009, Epigenomics.

[14]  S. Ariyan,et al.  Genome-wide screen of promoter methylation identifies novel markers in melanoma. , 2009, Genome research.

[15]  A. Feinberg,et al.  Genome-wide methylation analysis of human colon cancer reveals similar hypo- and hypermethylation at conserved tissue-specific CpG island shores , 2008, Nature Genetics.

[16]  E. Birney,et al.  An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). , 2008, Genome research.

[17]  A. Jimeno,et al.  Genome-wide profiling at methylated promoters in pancreatic adenocarcinoma , 2008, Cancer biology & therapy.

[18]  Thomas Lengauer,et al.  CpG Island Mapping by Epigenome Prediction , 2007, PLoS Comput. Biol..

[19]  M. Esteller.  Cancer epigenomics: DNA methylomes and histone-modification maps , 2007, Nature Reviews Genetics.

[20]  J. McPherson,et al.  Comprehensive DNA methylation profiling in a human cancer genome identifies novel epigenetic targets. , 2006, Carcinogenesis.

[21]  T. Rauch,et al.  MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells. , 2006, Cancer research.

[22]  Thomas Lengauer,et al.  ROCR: visualizing classifier performance in R , 2005, Bioinform..

[23]  A. Gnirke,et al.  Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis , 2005, Nucleic acids research.

[24]  Rafael A. Irizarry,et al.  Bioinformatics and Computational Biology Solutions using R and Bioconductor , 2005 .

[25]  W. Lam,et al.  Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells , 2005, Nature Genetics.

[26]  Terry Speed,et al.  Normalization of cDNA microarray data. , 2003, Methods.

[27]  Rafael A Irizarry,et al.  Exploration, normalization, and summaries of high density oligonucleotide array probe level data. , 2003, Biostatistics.

[28]  John Quackenbush.  Microarray data normalization and transformation , 2002, Nature Genetics.

[29]  Andrew P Feinberg,et al.  A genome-wide screen for normally methylated human CpG islands that can identify novel imprinted genes. , 2002, Genome research.

[30]  C Eng,et al.  Excessive CpG island hypermethylation in cancer cell lines versus primary human malignancies. , 2001, Human molecular genetics.

[31]  A. Rosenthal,et al.  Large-scale methylation analysis of human genomic DNA reveals tissue-specific differences between the methylation profiles of genes and pseudogenes. , 2000, Human molecular genetics.

[32]  J. Issa,et al.  Genome-wide identification of aberrantly methylated promoter associated CpG islands in acute lymphocytic leukemia , 2008, Leukemia.

[33]  Gordon K. Smyth,et al.  limma: Linear Models for Microarray Data , 2005 .

[34]  T. Gingeras,et al.  Microarray-based DNA methylation profiling: technology and applications , 2022 .